The gastrointestinal tract of humans is a complex ecosystem composed of numerous interacting cell populations belonging to three different cell complexes: the epithelium, the immune system and the resident bacterial microbiota. However, the presence of all three components is required for full physiological function. Genetic or functional alterations of any one component of this ecosystem can result in a broken alliance and subsequent GI pathology. Due to the importance of gut microbiota for the host, in the recent years many studies have been made to evaluate the interaction between...